Hello --
> I am currently working in the McCammon group. I am interested in using
> APBS with advanced Monte-Carlo(MC) sampling strategies. I have managed
> to link and run APBS from within the C code that performs the MC
> moves.
Great!
> 1) Is there a way to pass APBS the solution from the previous
> iteration? Would such a strategy be useful in reducing time for the
> new solution?
Yes, but it's not straightforward and it's not clear what sort of
speed-up it would give you. Let me know if you really want more details.
> 2) In the case of focussing calculations, a call to initMG destroys
> the pbe and pmg objects of the previous calculation. Is this necessary
> if the goal is to reuse or repopulate these objects for incremental
> solutions?
This isn't necessary; however, some arrays used within Vpmg get
overwritten during solution of the PDE. You would need to institute
checks for this behavior before reusing too many things.
> 3) Have any of the users implemented such incremental calculations or
> have insights about the best course of action to accomplish the above?
I've played around with this a bit. Many PB-based dynamics methods do
not update the electrostatic potential unless an atom moves more than a
particular distance. I've made some initial steps towards implementing
this in our parallel focusing setting; i.e., updating local/fine maps at
a different frequency than global/coarse maps based on atom
displacements. However, I do not currently have any estimate on errors
for these types of updates.
--
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone: (314) 362-2040, Fax: (314) 362-0234
URL: http://www.biochem.wustl.edu/~baker

Hi,
I am currently working in the McCammon group. I am interested in using
APBS with advanced Monte-Carlo(MC) sampling strategies. I have managed
to link and run APBS from within the C code that performs the MC
moves.
Since only a few atoms change positions from one snapshot to the next,
I was wondering if there was a way to speed up APBS for the
calculating the energies of the new configuration, namely perform
"incremental calculations", since the electrostatic field will be
largely the same at distances far away from the moved atoms. More
specifically, I had the following questions:
1) Is there a way to pass APBS the solution from the previous
iteration? Would such a strategy be useful in reducing time for the
new solution?
2) In the case of focussing calculations, a call to initMG destroys
the pbe and pmg objects of the previous calculation. Is this necessary
if the goal is to reuse or repopulate these objects for incremental
solutions?
3) Have any of the users implemented such incremental calculations or
have insights about the best course of action to accomplish the above?
Thanks,
Tushar.

These error messages come from the MALOC hardware abstraction library
that the APBS software uses for I/O, memory management, etc. These are
just warnings that the input file reader has hit the end of the PDB (or
APBS input) file. You should encounter these messages for most PDB
files; don't worry about them.
Thanks,
Nathan
vincentc@... wrote:
> All --
>
> I've been playing around with APBS trying to get a feel for it. One of
> the runs I've done was with a PDB file that I converted into a PQR file
> using the online PDB->PQR converter (http://agave.wustl.edu/pdb2pqr/).
> When I try running APBS on this converted PQR, I get the following error
> messages:
>
> ---
> asc_getToken: Error occurred (bailing out).
> Vio_scanf: Format problem with input.
> ---
>
> What is the origin of these error messages? They aren't fatal --- the
> APBS calculations continue and I do get an answer.
>
> Thanks,
>
> Vince
> _______________________________________________
> apbs-users mailing list
> apbs-users@...
> http://cholla.wustl.edu/mailman/listinfo/apbs-users
--
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone: (314) 362-2040, Fax: (314) 362-0234
URL: http://www.biochem.wustl.edu/~baker

All --
I've been playing around with APBS trying to get a feel for it. One of the
runs I've done was with a PDB file that I converted into a PQR file using
the online PDB->PQR converter (http://agave.wustl.edu/pdb2pqr/). When I
try running APBS on this converted PQR, I get the following error
messages:
---
asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
---
What is the origin of these error messages? They aren't fatal --- the APBS
calculations continue and I do get an answer.
Thanks,
Vince

The best place to start for the new accessibility functions is the Vacc
class (http://agave.wustl.edu/apbs/doc/html/programmer/group__Vacc.html).
This is where new accessibility functions should be implemented. Once you
get them implemented there, Todd and I would be happy to point you to the
way to access these modifications through the main driver.
The file mypde.f is fine to modify for a quick hack but it should be
possible to do something a bit more sophisticated as well. Since I don't
know what sorts of changes you are planning to make to the PDE, I can't
provide too much more information...
--
Nathan A. Baker, Assistant Professor
Washington University in St. Louis School of Medicine
Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology
700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110
Phone: (314) 362-2040, Fax: (314) 362-0234
URL: http://www.biochem.wustl.edu/~baker
> -----Original Message-----
> From: apbs-users-admin@...
> [mailto:apbs-users-admin@...] On Behalf Of
> vincentc@...
> Sent: Friday, February 11, 2005 3:03 AM
> To: apbs-users@...
> Subject: [Apbs-users] modifying APBS
>
> Hello APBS users ---
>
> I'm working in a group with APBS and we're looking into
> modifying a few of the routines to do a few things we're
> interested in. We have the source code, but would like to
> know where to make these changes. Primarily, we want to:
>
> * Modify the way APBS calculates the accesiblity function
> k(x) and the dielectric function e(x)
>
> * Modify the PDE that APBS seeks to solve
>
> We've taken a look in the code and found a chunk of code in
> mypde.f --- is this the only place that we need to look for
> changing the PDE?
>
> Thanks,
>
> Vince
> _______________________________________________
> apbs-users mailing list
> apbs-users@...
> http://cholla.wustl.edu/mailman/listinfo/apbs-users
>

Hello APBS users ---
I'm working in a group with APBS and we're looking into modifying a few of
the routines to do a few things we're interested in. We have the source
code, but would like to know where to make these changes. Primarily, we
want to:
* Modify the way APBS calculates the accesiblity function k(x) and the
dielectric function e(x)
* Modify the PDE that APBS seeks to solve
We've taken a look in the code and found a chunk of code in mypde.f --- is
this the only place that we need to look for changing the PDE?
Thanks,
Vince

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